Core-shell structured Ag/SiO2 nanocomposite has been synthesized by a cyclohexane/Igepal/water reverse micelle system. The spherical nanocomposite particles were washed and concentrated with high performance liquid chromatography (HPLC) to remove the surfactant added during synthesis. Spherical SiO2 micrometer-scale particles were packed in the HPLC column as a stationary phase for the washing and dispersing of Ag/SiO2 nanocomposite particles. Surface modification of Ag/SiO2 nanocomposite particles and SiO2 microspheres with silane coupling agent enhanced the surface charge of the particles and improved the efficiency of washing with HPLC. Well-dispersed Ag/SiO2 stable suspensions were successfully attained in ethanol/ water mixed solvents after HPLC washing. The state of dispersion for the Ag/SiO2 nanocomposite suspension was systematically assessed using dynamic light scattering (DLS) and transmission electron microscope (TEM) and spin coat/atomic force microscope (AFM) analyses. The mechanism of the enabling HPLC washing protocol for SiO2-based nanoparticles is discussed.